Essential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes

In this repository you can find the code used for processing the raw sequence data, and for predicting essential genes using TraDIS in P. limnophila, based on Goodall, E.C.A. et al. "The Essential Genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.

How to use the code

Make sure all the necessary software and packages are installed (see requirements.txt for details). Then, download the raw data and run in the following order:

1. insertions_pipeline.sh
2. data_processing.R
3. stats_insertions.sh
4. tradis.R
5. stats_essentiality.sh
6. domain_essential.py

You will also need the genome of interest, in this case that of P. limnophila, in .gff3 and .fna format. For this .fna, you will need to create a bowtie index using bowtie2-build. See bowtie2 documentation.

Credits

This project has been developed thanks to the effort and contribution of the following individuals:

• David Moyano Palazuelo - Link to GitHub Profile
• Ildefonso Cases

We appreciate everyone who has dedicated their time and expertise to improve this project and make it possible.